Well, Emma was faking the car issues, wasn't she? So we don't really know what would have happened if she really tried. But yeah, I thought that she assumed Emma could leave since she could come to town in the first place. But with this latest episode, I have the feeling that there's more consequences to leaving Storybrooke than fairly minor car crashes - something more along the lines of Granny having a heart attack because Ruby left. Likely that other something bad would have happened to the kids (and Emma, Regina was probably hoping).

I really don't think she was secretly wanting the family back together. Even if she didn't already dislike them for turning her down in FTL, the dad not wanting to claim them goes against her "you don't abandon family" reasoning in the Hatter's episode so I doubt she was secretly on his side.